This review is mainly concerned with a whole-genome association scan, using single nucleotide polymorphisms (SNPs), for a dichotomous disease status. It will be clear, however, that many of the methods apply in other situations, in particular to array expression studies. Although there are important differences between these two applications -- including the number of expected true associations, sample size and effect size (Table 1) -- their common exploratory character suggests that further advances may arise from crossapplication of ideas between these areas. For this reason, some methods developed for expression studies are reviewed; there is also a discussion on whether they may be suitable for genetic association scans. The objects of inference used will be 'genes'[18], with the understanding that, in this context, this can mean SNPs, whole genes, haplotype blocks, transcript levels or other features.
